1. Field of the Invention
The present invention relates to a method for displaying results of hybridization experiments in which a biochip is used to hybridize a sample biopolymer with a probe biopolymer with a known sequence.
2. Detailed Description of the Prior Art
Biochips, also known as DNA micro arrays, have been developed to simultaneously quantify various biopolymer species, such as DNA sequences, that are present in a sample in different volumes. The technology is overviewed in Vivian G. Cheung et al., “Making and reading microarrays,” Nature Genetics Supplement, vol. 21, January 1999. In a typical biochip technique, different probe biopolymers, for example, DNA molecules, are immobilized on a surface of a support such as glass slides and, through hybridization, selectively bind to different labeled biopolymers, for example, DNA sequences, in a sample. Specific sample biopolymers can be quantified based on the amounts of markers that have been selectively coupled to the probe biopolymers via sample biopolymers hybridized to the probe biopolymers. This principle makes it possible to quantify many different sample biopolymers at a time by immobilizing many different probe biopolymers on the same support.
In order for two DNA sequences to hybridize, the two sequences need to have base sequences complementary, or nearly complementary, to one another. When hybridized, the complementary strands have a high binding energy and are stable at a certain temperature. This binding energy varies depending on the length and base composition (GC content) of the strand. Two hybridized strands with partially non-complementary sequences can also have a sufficiently high binding energy when they contain complementary regions of sufficient lengths. This means that there is a chance that sample DNA molecules of the same type bind to two different types of DNA probes that are very similar to one another. It is known that the likelihood that this unintended hybridization (miss-hybridization) occurs varies depending on the conditions of hybridization experiments.
A type of biochips that uses synthetic short DNA strands as DNA probes is known (oligonucleotide array). In this type of biochips, DNA molecules with sequences similar to respective subject DNA probes are synthesized and used to serve as DNA probes for comparison so as to determine if the hybridized sample DNA is the intended sequence as the target of the subject DNA probe. This technique is reviewed by Robert J. Lipshutz et al (Robert J. Lipshutz et al.: High density synthetic oligonucleotide arrays, Nature Genetics Supplement, Vol. 21, January 1999).
However, in biochips that use longer DNA molecules, such as cDNA, as a probe biopolymer, no effective technique is known that can evaluate the results of hybridization using DNA sequence data.
The Smith-Waterman method is a known technique for searching for regions with highest homology between two different DNA sequences (Smith, T. F. and Waterman, M. S.: J. Mol. Biol. 147, 195–197, 1981). Also, methods are known such as BLAST that allow for a fast search for a target sequence having a high homology with a DNA sequence of interest (key sequence) among many different DNA sequences (targets) (Altschul et al., Nucleic Acids Res., 25, 3389–3402, 1997). Many other algorithms have been developed for the same purpose. In these approaches, the degrees of homology between two DNA sequences are expressed by indices such as “homology score,” which is based on the scores used in the search for high homology regions between the two DNA sequences, or by “matching rate,” which is based on the proportion of the complementary DNA portions in the region (these indices, each representing the degree of homology, are collectively referred to as “similarity score,” hereinafter.).
In a technique widely used for data analysis of biochip experiments, subject DNA proves are statistically classified (i.e., clustered) based on the changes in levels of hybridization in a plurality of biochips. In the expression analysis for yeast conducted by P. Brown's group of the Stanford University, a DNA sample was prepared at each stage of cell development in a time-sequential manner and the samples were each hybridized to separate biochips. Types and the amounts of DNA sequences present in the DNA samples were determined for each stage. The DNA sequences (DNA probes) were then clustered based on the changes in amounts at each stage (Michel B. Eisen et al.: Cluster analysis and display of genome-wide expression patterns: Proc. Natl. Acad. Sci. (1998) Dec. 8, 1995 (25), 14863-8). The results are displayed in a tree diagram obtained from the clustering that indicates the order of clusters in the DNA sequence and the distances between the clusters. The results also include information about the DNA sequences (e.g., name, definitions, or the like) and hybridization patterns indicating the levels of hybridization for each DNA sequence on each of the biochips.
At present, no practical approach is known for determining if a probe biopolymer has been accurately hybridized to a sample biopolymer of interest, and accordingly, there is a need for such a method.